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Although cumulative N2O emissions are greater in the winter fallow season than in the rice-growing period, the mechanisms by which the emissions affect fallow paddy fields remain unclear. We aimed to identify N2O flux characteristics and illustrate how key nirS-, nirK- and nosZ-containing denitrifiers affect N2O emission levels in acidic fallow paddy soil. Five water-filled pore space (WFPS) levels were set at 25%, 50%, 75%, 100% and 125%, respectively. During the 48-h-long, high-flux incubation period, the N2O flux was the highest in soil samples with 75% WFPS, followed by those with 100% WFPS. The size of nirS-containing denitrifier community was more sensitive to the shifts in soil moisture and showed a stronger correlation with N2O flux than that of nirK-containing denitrifiers, whereas higher N2O concentrations induced an increase in the levels of nosZ-containing bacteria. After incubation for 48 h, nirK- and nosZ-denitrifying bacterial composition varied remarkably under 50%, 75%, and 100% WFPS treatments. However, the composition of nirS-containing denitrifying bacterial community gradually varied with an increase in soil moisture from 25% to 100% WFPS. Certain dominant OTUs of nirK- nirS- and nosZ-containing denitrifiers were highly abundant, especially under treatments of 50%, 75% and 100% WFPS, which were closely associated with the N2O flux. Thus, nirK, nirS and nosZ-containing denitrifiers respond to soil moisture differently, and enriched species might mainly be involved in controlling N2O flux in fallow paddy soils via denitrification, while the abundance of nirS-containing denitrifiers might affect N2O emission levels more significantly than that of nirK-containing denitrifiers. [ABSTRACT FROM AUTHOR]

Agricultural management significantly affects methane (CH4) and nitrous oxide (N2O) emissions from paddy fields. However, little is known about the underlying microbiological mechanism. Field experiment was conducted to investigate the effect of the water regime and straw incorporation on CH4 and N2O emissions and soil properties. Quantitative PCR was applied to measure the abundance of soil methanogens, methane-oxidising bacteria, nitrifiers, and denitrifiers according to DNA and mRNA expression levels of microbial genes, including mcrA, pmoA, amoA, and nirK/nirS/nosZ. Field trials showed that the CH4 and N2O flux rates were negatively correlated with each other, and N2O emissions were far lower than CH4 emissions. Drainage and straw incorporation affected functional gene abundance through altered soil environment. The present (DNA-level) gene abundances of amoA, nosZ, and mcrA were higher with straw incorporation than those without straw incorporation, and they were positively correlated with high concentrations of soil exchangeable NH4+ and dissolved organic carbon. The active (mRNA-level) gene abundance of mcrA was lower in the drainage treatment than in continuous flooding, which was negatively correlated with soil redox potential (Eh). The CH4 flux rate was significantly and positively correlated with active mcrA abundance but negatively correlated with Eh. The N2O flux rate was significantly and positively correlated with present and active nirS abundance and positively correlated with soil Eh. Thus, we demonstrated that active gene abundance, such as of mcrA for CH4 and nirS for N2O, reflects the contradictory relationship between CH4 and N2O emissions regulated by soil Eh in acidic paddy soils. [ABSTRACT FROM AUTHOR]

Objective: Paddy soils contain relatively greater organic matter and water contents than other soils thereby limiting effective mRNA extraction. A modification of the conventional mRNA soil extraction method specific to paddy soils is described. Results: Two main modifications for co-extraction of DNA and RNA are: (1) addition of 20 % (w/v) sodium dodecyl sulphate to 10 % (w/v) hexadecyltrimethylammonium bromide extraction buffer, and (2) fresh soil, initially frozen at −80 °C, is immediately immersed in extraction buffer. The high-quality total RNA extracted can be directly used in downstream analyses without an additional step to remove humic acid. RNA purification was conducted to remove 5S rRNA, and the mRNA was enriched by selectively digesting rRNA. cDNA synthesised by reverse transcriptase was not contaminated by the reagents or genomic DNA. Conclusion: The modified method for mRNA extraction from paddy soil is suitable for analysing the expression of microbial genes from fresh paddy soil. [ABSTRACT FROM AUTHOR]

Purpose: Soils derived from different parent materials are known to support quite distinct indigenous community structures. Crop cultivation is also an important factor regulating bacterial community structure in soils. However, the extent to which the soil parent material imposes limits on the diversity of organisms present and the extent to which cropping practices are able to supplant the effects of soil parent materials are largely unknown. Materials and methods: Five ancient paddy soils developed on three different parent materials were collected from the major rice production regions in southern China. The 16S rRNA genes were amplified from each soil DNA sample and then analyzed using Tag-pyrosequencing and terminal restriction fragment length polymorphism (T-RFLP) to characterize bacterial communities and their relative abundance. Total bacterial abundance was determined by 16S rRNA gene quantitative PCR (qPCR). Canonical correspondence analysis (CCA) was used to investigate the relationship between the bacterial distribution and soil properties. Results and discussion: Cluster analysis of the T-RFLP and pyrosequencing data indicated that although the bacterial communities in the surface layers (0-20 cm) could be distinguished from those recovered from depths of 20-40 and 40-60 cm in all soils, the bacterial community structures in soils with similar parent materials clustered regardless of soil depth. Bacteria of the phylum Proteobacteria dominated in all soils with significantly higher proportions in the top soils. The relative abundances of Chloroflexi and Acidobacteria were closely associated with the soil parent material. This suggested that the changes in bacterial community compositions induced by rice cultivation did not mask those determined by soil parent material. CCA indicated that soil pH, available Mn, and total K and Fe contents explained most of the variance in bacterial distribution due to differences in parent materials. qPCR revealed that the bacterial abundance in top soils (0-20 cm) also varied with parent material. Conclusions: The nature of the parent material is an important factor in determining soil bacterial community structure, and although long-term rice cultivation resulted in shifts in this structure, the community retained characteristics of the original populations. [ABSTRACT FROM AUTHOR]

Purpose: Soil microbial communities can be strongly influenced by agricultural practices, but little is known about bacterial community successions as land use changes. The objective of this study was to determine microbial community shifts following major land use changes in order to improve our understanding of land use impacts on microbial community composition and functions. Materials and methods: Four agricultural land use patterns were selected for the study, including old rice paddy fields (ORP), Magnolia nursery planting (MNP), short-term vegetable (STV), and long-term vegetable (LTV) cultivation. All four systems are located in the same region with same soil parent material (alluvium), and the MNP, STV, and LTV systems had been converted from ORP for 10, 3, and 30 years, respectively. Soil bacteria and ammonia oxidizer community compositions were analyzed by 454 pyrosequencing and terminal restriction fragment length polymorphism, respectively. Quantitative PCR was used to determine 16S rRNA and amoA gene copy numbers. Results and discussion: The results showed that when land use was changed from rice paddy to upland systems, the relative abundance of Chloroflexi increased whereas Acidobacteria decreased significantly. While LTV induced significant shifts of bacterial composition, MNP had the highest relative abundance of genera GP1, GP2, and GP3, which were mainly related to the development of soil acidity. The community composition of ammonia-oxidizing bacteria (AOB) but not ammonia-oxidizing archaea was strongly impacted by the agricultural land use patterns, with LTV inducing the growth of a single super predominant AOB group. The land use changes also induced significant shifts in the abundance of 16S rRNA and bacterial amoA genes, but no significant differences in the abundance of archaea amoA was detected among the four land use patterns. Soil total phosphorous, available phosphorous, NO, and soil organic carbon contents and pH were the main determinants in driving the composition of both bacteria and AOB communities. Conclusions: These results clearly show the significant impact of land use change on soil microbial community composition and abundance and this will have major implications on the microbial ecology and nutrient cycling in these systems, some of which is unknown. Further research should be directed to studying the impacts of these microbial community shifts on nutrient dynamics in these agroecosystems so that improved nutrient management systems can be developed. [ABSTRACT FROM AUTHOR]

• Under high NH 4 NO 3 availability, paddy soils with 125% WFPS produced the highest N 2 O. • Denitrification was the dominant process to N 2 O flux during rice growing seasons. • A few key taxa of nirK - and nosZ -containing denitrifiers mitigate N 2 O emissions. Debate persists regarding the underlying factors influencing nitrous oxide (N 2 O) emissions and their mechanisms of action in rice paddy soils. The aim of the present study was to delineate the contributions of nitrification and denitrification to N 2 O emissions in acidic paddy soils under adequate N fertilisation. To identify the key taxa associated with N 2 O emissions and explore the potential underlying mechanisms, we performed stable N isotope (15N) tracing, quantitative PCR, and Illumina MiSeq sequencing of amoA , nirK , nirS, and nosZ genes. Under sufficient NH 4 NO 3 input, soil N 2 O emissions increased significantly with an increase in soil moisture, peaking at 125% water-filled pore space (WFPS). N 2 O flux was positively associated with potential denitrification rates but not potential nitrification rates. The relative contribution of denitrification to N 2 O emissions increased with an increase in soil moisture and reached more than 90% at 75%, 100%, and 125% WFPS during the 96 h of incubation. Based on relative abundance and connectivity degree of operational taxonomic units, soil moisture-enhanced N 2 O emissions were strongly correlated with only a few key taxa, including nirK -containing denitrifiers belonging to Bradyrhizobium , as well as nosZ -containing denitrifiers belonging to Tardiphaga. In conclusion, denitrification could play a more dominant role in N 2 O emissions than nitrification in acidic paddy soil under sufficient NH 4 NO 3 inputs, and the effects of soil moisture on N 2 O emissions could be attributed to a few key nirK - and nosZ -denitrifier taxa, through shifts in community composition and synergistic interactions of network structures between them. [ABSTRACT FROM AUTHOR]